Computational Systems Biology course

CSB course Wiki

This is the CSB course wiki, here you will find the latest course material.

Contacts

Lecturer:
Prof. Igor Goryanin - goryanin at inf.ed.ac.uk

Teaching Assistants:
Hongwu Ma - hma2 at inf.ed.ac.uk
Anatoly Sorokin - asorokin at inf.ed.ac.uk

Systems Biology.
What is it?

Listen to Nature's Systems Biology podcast

CSB Lectures outline

Lecture 1 - Introduction to Systems Biology

Lecture 2 - Chemical Foundation and Enzymes

Atoms and Bonds
Chemical reactions
Thermodynamics
Enzyme structure
Enzyme nomenclature
Free energy in enzymatic reactions

Lecture 3 - Enzyme kinetics

Simple enzyme kinetics
Steady-state rate equations
Reactions of two substrates
Inhibition of enzyme activity
pH dependence
Biological regulation of enzymes

Lecture 4 - Metabolic Pathways

Glycolysis
Pathway databases (KEGG, Metacyc)
Proteins regulating proteins (phosphorylation, transcriptional regulation and signal transduction)

Lecture 5 - Flux balance analysis

A quick revision of the law of mass action
How to represent metabolic networks:
- Stochiometric coefficients
- The stochiometric matrix
- System equations
A way of simplifying the cell metabolic complexity: Flux Balance Analysis

Lecture 6 - Metabolic Control Analysis

Reductionist vs. Systems theory
- Regulation and control
- Time scales
- Metabolic Steady states
Metabolic Control Analysis
- Flux Control Coefficients
- The Summation theorem
- Metabolites effects and Elasticities
- The Connectivity theorem
- Response Coefficients
Conclusion: MCA vs. traditional approaches

Lecture 7 - Metabolic Network Reconstruction

Genome based reconstruction of metabolic networks
useful databases
Improve the quality of the reconstructed network
Graph representation of metabolic network

Lecture 8 - Network structure analysis

Structural prameters of large scale network
- Connection degree distribution (Scale free network)
- Average path length
- Node centrality and network centrality
Global connectivity of the network (Connected component and Bow-tie structure)
Modules in the network (Network decomposition)
Software and tools for network structure analysis

Lecture 9 - Gene regulatory network

Methods for regulatory network reconstruction
Useful databases
Multi-layer hierarchical structure of regulatory network
Network motifs
Integrated network

Lecture 10 - Kinetic model of gene circuit

kinetic equations for gene regulation
Simple gene regulation model
Combinatorial gene regulation model
Feed forward loop model
Synthetic biology and artificial gene circuits
SBML, software and databases for modelling

Lecture 11 - Signal Transduction

Introduction on cell signalling
Metabolism vs. Signal transduction
The signalling paradigm and some typical components:
- The receptor
- G protein
- MAP kinase cascade

Lecture 12 - Dynamic Signalling and Gene Expression Regulation

Modelling of molecular networks: Simple modules for building complex dynamic networks
Signal response curves:
- Linear and hyperbolic
- Sigmoidal (buzzer)
- Perfectly adapted (sniffer)
- Positive feedback
- - Mutual activation (one way switch)
  - Mutual inhibition (toggle switch)
- Negative feedback
- - homeostasis
  - oscillations (Blinker)
Modelling Gene Expression Regulation with:
- Ordinary differential equations
- Directed and undirected graphs
- Bayesian networks
- Boolean networks